Workshop Working Groups: Difference between revisions
No edit summary |
(cleaned up text, added group pages/channel links) |
||
| Line 4: | Line 4: | ||
* Group Page: [[Computable Graphs]] | * Group Page: [[Computable Graphs]] | ||
* Project Pages: [[Translate Logseq Knowledge Graph to Systems Biology Network Diagrams]] | * Project Pages: | ||
* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983137222467604 # | ** [[Translate Logseq Knowledge Graph to Systems Biology Network Diagrams]] | ||
** [[Synthesis center for cell biology]] | |||
* Discord Channel: [https://discord.com/channels/1029514961782849607/1038983137222467604 #computable-graphs] | |||
=== What === | === What === | ||
| Line 13: | Line 15: | ||
Discussion entry points: | Discussion entry points: | ||
[[Matthew Akamatsu]] https://discord.com/channels/1029514961782849607/1033091746139230238/1040212464631029822 | * [[Matthew Akamatsu]] https://discord.com/channels/1029514961782849607/1033091746139230238/1040212464631029822 | ||
=== Who === | === Who === | ||
[[Konrad Hinsen]], based on work on leibniz-pharo and interest in computational modeling/research | * [[Akila Wijerathna-Yapa]] | ||
* [[Matthew Akamatsu]] (lead?) | |||
* [[Konrad Hinsen]], based on work on leibniz-pharo and interest in computational modeling/research | |||
* [[Jodi Schneider]]? | |||
[[Jodi Schneider]]? | |||
=== Progress so far === | === Progress so far === | ||
Some resources: | |||
https:// | * Simularium https://simularium.allencell.org/ | ||
* Vivarium Collective https://vivarium-collective.github.io/ | |||
Vivarium Collective https://vivarium-collective.github.io/ | |||
=== Next (ideas for next steps, open problems) === | === Next (ideas for next steps, open problems) === | ||
don't know if a joint project makes sense, but perhaps coordinated first prototypes of a bridge | don't know if a joint project makes sense, but perhaps coordinated first prototypes of a bridge? | ||
could use: | could use: | ||
someone with programming skills to implement a POC translation between a discourse graph and one of the specific modeling languages/ontologies | * someone with programming skills to implement a POC translation between a discourse graph and one of the specific modeling languages/ontologies | ||
== Synthesis-oriented social media aka "from the stream to the garden" == | == Synthesis-oriented social media aka "from the stream to the garden" == | ||
| Line 63: | Line 60: | ||
=== Who === | === Who === | ||
* [[Ronen Tamari]] (lead?) | |||
* [[Konrad Hinsen]] | |||
[[Konrad Hinsen]] | * [[Jonny Saunders]] | ||
* this seems super relevant to [[Amy Zhang]] based on prior work on Wikum and Tilde | |||
[[Jonny Saunders]] | * and [[Nouran Soliman]] based on LiTweeture project | ||
* and [[Michael Toomim]] and team based on their work on peeryview | |||
this seems super relevant to [[Amy Zhang]] based on prior work on Wikum and Tilde | |||
and [[Nouran Soliman]] based on LiTweeture project | |||
and [[Michael Toomim]] and team based on their work on peeryview | |||
=== Progress so far === | === Progress so far === | ||
Resources | Resources | ||
BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/ | * BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/ | ||
* [[Fediverse]] | |||
[[Fediverse]] | * [[Mastodon]] | ||
* [[ActivityPub]] | |||
[[Mastodon]] | |||
[[ActivityPub]] | |||
[[ | [[Benjamin Goering]] started a thread with a prototype of expressing a graph of info using both ActivityStreams and SEPIO ontologies - https://discord.com/channels/1029514961782849607/1033091723389317160/1040042059916120094 | ||
=== Next (ideas for next steps, open problems) === | === Next (ideas for next steps, open problems) === | ||
| Line 97: | Line 84: | ||
could use: | could use: | ||
a "user" (preferably non-technical) to give feedback on mental models here. maybe | * a "user" (preferably non-technical) to give feedback on mental models here. maybe [[Pooja Upadhyay]]? | ||
== Extending semantic mediawiki to cover discourse graph modeling == | == Extending semantic mediawiki to cover discourse graph modeling == | ||
| Line 108: | Line 95: | ||
It could be really valuable to try to prototype a "computable" synthesis of the knowledge in this workshop here in the wiki. One test of the "computability" would be to make it visualizable. | It could be really valuable to try to prototype a "computable" synthesis of the knowledge in this workshop here in the wiki. One test of the "computability" would be to make it visualizable. | ||
Could have applications to thesemantic climate setting that [[Peter- | Could have applications to thesemantic climate setting that [[Peter Murray-Rust]] is working on | ||
See discussion in <code>#discourse-modeling</code> channel | See discussion in <code>#discourse-modeling</code> channel | ||
| Line 116: | Line 103: | ||
=== Who === | === Who === | ||
[[Kyle | * [[Kyle MacLaury]] | ||
* [[Peter Murray-Rust]] | |||
[[Peter- | * [[Karola Kirsanow]]? | ||
* [[Joel Chan]] also interested in assisting | |||
[[Karola Kirsanow]]? | |||
[[Joel Chan]] also interested in assisting | |||
=== Progress so far === | === Progress so far === | ||
| Line 128: | Line 112: | ||
* [[Discourse Modeling]] | * [[Discourse Modeling]] | ||
* [[Making Discourse Graphs Indexable & Discoverable]] | * [[Making Discourse Graphs Indexable & Discoverable]] | ||
=== Next (ideas for next steps, open problems) === | === Next (ideas for next steps, open problems) === | ||
= Latent/forming = | = Latent/forming = | ||
| Line 146: | Line 124: | ||
=== What === | === What === | ||
How do we define minimal information models tuned for synthesis that can interoperate across various disciplines? | |||
Concrete problem expressed by [[Peter-Murray Rust]] here: https://discord.com/channels/1029514961782849607/1040214388554084372/1040299259930611833: "The idea of Hypothesis testing is common in some disciplines, unknown in others. For example chemical synthesis or materials science is "can we make X?" and many sciences are exploratory - what can we see with a new telescope, plants in Antarctica, etc. You have to design your project but I suspect Hypothesis doesn't come into it." | |||
And to a certain extent, the issue of representing/discussing the discourse of computational research (e.g., model parameters), discussed by [[Konrad Hinsen]] here: https://discord.com/channels/1029514961782849607/1038988750677606432/1039576903838859326 | |||
This connects also with [[Peter-Murray Rust]]'s work on semantic climate (semantifying the IPCC report). | |||
* see discussion here: https://discord.com/channels/1029514961782849607/1040057721044598788/1040060670907002973 | |||
* and here: https://discord.com/channels/1029514961782849607/1033091746139230238/1040226423346040853 | |||
And also connects to emerging discussions around interoperability and Surfacing/managing/resolving disagreements in ontologies/terms/federation | |||
=== Who === | |||
And [[Paul Itoi]] based on interest in multiplayer zettelkastens | * [[Joel Chan]] is definitely interested in this, happy to lead this | ||
* [[Peter Murray-Rust]]? | |||
* Possibly also [[James Howison]], based on emphasis in workshop submission on software artifacts as a locus of synthesis | |||
* And [[Paul Itoi]] based on interest in multiplayer zettelkastens | |||
=== Progress so far === | === Progress so far === | ||
=== Next (ideas for next steps, open problems) === | === Next (ideas for next steps, open problems) === | ||
| Line 187: | Line 162: | ||
=== Who === | === Who === | ||
[[Jordan Wick]], based on work on "explain paper like i'm 5": https://github.com/epli-org/epli | * [[Elianna DeSota]]: https://discord.com/channels/1029514961782849607/1033091572167888926/1036629378567770223 - "I would love to explore how we might better navigate the increasing 'bits' of knowledge and research that we are publishing and sharing among our communities, and new + better ways of thinking about how to synthesize and evaluate the relationships between different fields of research." | ||
* [[Joseph Chee Chang]]: https://discord.com/channels/1029514961782849607/1033091572167888926/1040001880002154546 | |||
* [[Jordan Wick]], based on work on "explain paper like i'm 5": https://github.com/epli-org/epli | |||
=== Progress so far === | === Progress so far === | ||
| Line 206: | Line 183: | ||
=== Who === | === Who === | ||
* [[Matt Clancy]]: https://discord.com/channels/1029514961782849607/1033091746139230238/1037560902800658514 | |||
* [[Eirini Malliaraki]] | |||
[[ | |||
[[ | |||
[[ | * [[Martin Karlsson]]: https://discord.com/channels/1029514961782849607/1033091746139230238/1039238852721770556 | ||
* [[Karola Kirsanow]]: https://discord.com/channels/1029514961782849607/1033091746139230238/1039228139366268938 | |||
* [[Matthew Evans]]: https://discord.com/channels/1029514961782849607/1033091597635694694/1036658723596279868 | |||
[[Wayne Lutters]]? | * [[Pao Siangliulue]], based on past work on integrated crowdsourcing | ||
* Maybe also and [[Nouran Soliman]] based on LiTweeture project | |||
* And [[Angelina Lesnikova]] and [[Valerii Kremnev]] based on the sci2sci approach of integrating publishing into lab notebooks | |||
* [[Jay Patel]], based on expressed interests in reimagining peer review processes | |||
* [[Wayne Lutters]]? | |||
=== Progress so far === | === Progress so far === | ||
=== Next (ideas for next steps, open problems) === | === Next (ideas for next steps, open problems) === | ||
| Line 235: | Line 209: | ||
=== Who === | === Who === | ||
[[Konrad Hinsen]] and [[Jonny Saunders]]: https://discord.com/channels/1029514961782849607/1038988750677606432/1040172075773607956 | * [[Konrad Hinsen]] and [[Jonny Saunders]]: https://discord.com/channels/1029514961782849607/1038988750677606432/1040172075773607956 | ||
=== Progress so far === | === Progress so far === | ||
| Line 242: | Line 216: | ||
== Hidden value / mental model mismatches in transitions between workflows / tools == | == Hidden value / mental model mismatches in transitions between workflows / tools == | ||
* Group page: [[Mental Models]] | |||
* Discord Channel: [https://discord.com/channels/1029514961782849607/1040470706271555706 #mental-models] | |||
=== What === | === What === | ||
What hidden value / mental | What hidden value / mental (mis)matches might there be between new infrastructures we want to build (e.g., ontology-based organization of knowledge) and existing workflows / tools amongst scientists? | ||
=== Who === | === Who === | ||
[[Pooja Upadhyay]]: https://discord.com/channels/1029514961782849607/1038594946791387276/1039242312615735346 | [[Pooja Upadhyay]]: https://discord.com/channels/1029514961782849607/1038594946791387276/1039242312615735346 | ||
| Line 254: | Line 230: | ||
twitter (centralized platform) to mastodon (decentralization, federation) | twitter (centralized platform) to mastodon (decentralization, federation) | ||
[[Peter- | [[Peter Murray-Rust]] | ||
e.g., ontologies vs. dictionaries | e.g., ontologies vs. dictionaries | ||
Revision as of 03:56, 11 November 2022
Coalesced
Integrating/bridging narrative/discourse with computable knowledge graphs (and back)
- Group Page: Computable Graphs
- Project Pages:
- Discord Channel: #computable-graphs
What
How to ground knowledge graphs (that can be used for prediction or computational simulation experiments and models) in the discourse of evidence in scientific literature? How to transition from unstructured literature to knowledge graphs and keep things updated with appropriate provenance for (un)certainty?
Discussion entry points:
- Matthew Akamatsu https://discord.com/channels/1029514961782849607/1033091746139230238/1040212464631029822
Who
- Akila Wijerathna-Yapa
- Matthew Akamatsu (lead?)
- Konrad Hinsen, based on work on leibniz-pharo and interest in computational modeling/research
- Jodi Schneider?
Progress so far
Some resources:
- Simularium https://simularium.allencell.org/
- Vivarium Collective https://vivarium-collective.github.io/
Next (ideas for next steps, open problems)
don't know if a joint project makes sense, but perhaps coordinated first prototypes of a bridge?
could use:
- someone with programming skills to implement a POC translation between a discourse graph and one of the specific modeling languages/ontologies
Synthesis-oriented social media aka "from the stream to the garden"
- Group Page: Synthesizing Social Media
- Project Pages: Linked Data Publishing On Activitypub
- Discord Channel: #linked-data-activitypub
What
How to enable sharing/direction of scholarly attention in a synthesis-oriented manner (e.g., not just popularity, but relevance to questions/hypotheses/methods, etc.)?
context in discussions on Discord:
https://discord.com/channels/1029514961782849607/1033091723389317160/1037771875012591616
concrete example: https://discord.com/channels/1029514961782849607/1037786518800039978/1037791239908622466
SEPIO + ActivitySteams via JSON-LD: https://discord.com/channels/1029514961782849607/1040042059916120094/1040042094363942932
Who
- Ronen Tamari (lead?)
- Konrad Hinsen
- Jonny Saunders
- this seems super relevant to Amy Zhang based on prior work on Wikum and Tilde
- and Nouran Soliman based on LiTweeture project
- and Michael Toomim and team based on their work on peeryview
Progress so far
Resources
- BookWyrm: Social Reading and Reviewing https://joinbookwyrm.com/
- Fediverse
- Mastodon
- ActivityPub
Benjamin Goering started a thread with a prototype of expressing a graph of info using both ActivityStreams and SEPIO ontologies - https://discord.com/channels/1029514961782849607/1033091723389317160/1040042059916120094
Next (ideas for next steps, open problems)
there seems to be some energy behind producing a prototype/spec, perhaps to implement in an ActivityPub base
could use:
- a "user" (preferably non-technical) to give feedback on mental models here. maybe Pooja Upadhyay?
Extending semantic mediawiki to cover discourse graph modeling
- Group page: Discourse Modeling
- Discord Channel: #discourse-modeling
What
It could be really valuable to try to prototype a "computable" synthesis of the knowledge in this workshop here in the wiki. One test of the "computability" would be to make it visualizable.
Could have applications to thesemantic climate setting that Peter Murray-Rust is working on
See discussion in #discourse-modeling channel
Entry point: https://discord.com/channels/1029514961782849607/1039384335423389836/1039388306208718938
Who
- Kyle MacLaury
- Peter Murray-Rust
- Karola Kirsanow?
- Joel Chan also interested in assisting
Progress so far
Next (ideas for next steps, open problems)
Latent/forming
Information models for (collaborative) interdisciplinary synthesis
- Group page: Interdisciplinary Models
- Discord Channel: #interdisciplinary-models
What
How do we define minimal information models tuned for synthesis that can interoperate across various disciplines?
Concrete problem expressed by Peter-Murray Rust here: https://discord.com/channels/1029514961782849607/1040214388554084372/1040299259930611833: "The idea of Hypothesis testing is common in some disciplines, unknown in others. For example chemical synthesis or materials science is "can we make X?" and many sciences are exploratory - what can we see with a new telescope, plants in Antarctica, etc. You have to design your project but I suspect Hypothesis doesn't come into it."
And to a certain extent, the issue of representing/discussing the discourse of computational research (e.g., model parameters), discussed by Konrad Hinsen here: https://discord.com/channels/1029514961782849607/1038988750677606432/1039576903838859326
This connects also with Peter-Murray Rust's work on semantic climate (semantifying the IPCC report).
- see discussion here: https://discord.com/channels/1029514961782849607/1040057721044598788/1040060670907002973
- and here: https://discord.com/channels/1029514961782849607/1033091746139230238/1040226423346040853
And also connects to emerging discussions around interoperability and Surfacing/managing/resolving disagreements in ontologies/terms/federation
Who
- Joel Chan is definitely interested in this, happy to lead this
- Peter Murray-Rust?
- Possibly also James Howison, based on emphasis in workshop submission on software artifacts as a locus of synthesis
- And Paul Itoi based on interest in multiplayer zettelkastens
Progress so far
Next (ideas for next steps, open problems)
Synthesis-oriented search/discovery/exploration user interfaces
- Group Page: Interfaces
- Discord Channel: #interfaces
What
How do we support richer forms of synthesis-oriented interaction with the existing bodies of research that transcend publications as the unit?
Who
- Elianna DeSota: https://discord.com/channels/1029514961782849607/1033091572167888926/1036629378567770223 - "I would love to explore how we might better navigate the increasing 'bits' of knowledge and research that we are publishing and sharing among our communities, and new + better ways of thinking about how to synthesize and evaluate the relationships between different fields of research."
- Joseph Chee Chang: https://discord.com/channels/1029514961782849607/1033091572167888926/1040001880002154546
- Jordan Wick, based on work on "explain paper like i'm 5": https://github.com/epli-org/epli
Progress so far
Resources
Next (ideas for next steps, open problems)
Social infrastructures for synthesis (e.g., incentives, funding)
- Wiki Page: Social Systems
- Discord Channel: #social-systems
What
How to design/foster social structures / incentives / programs for fostering synthesis-friendly work, such as writing living literature reviews, adding metadata to experiments, etc.?
Who
- Matt Clancy: https://discord.com/channels/1029514961782849607/1033091746139230238/1037560902800658514
- Eirini Malliaraki
- Martin Karlsson: https://discord.com/channels/1029514961782849607/1033091746139230238/1039238852721770556
- Karola Kirsanow: https://discord.com/channels/1029514961782849607/1033091746139230238/1039228139366268938
- Matthew Evans: https://discord.com/channels/1029514961782849607/1033091597635694694/1036658723596279868
- Pao Siangliulue, based on past work on integrated crowdsourcing
- Maybe also and Nouran Soliman based on LiTweeture project
- And Angelina Lesnikova and Valerii Kremnev based on the sci2sci approach of integrating publishing into lab notebooks
- Jay Patel, based on expressed interests in reimagining peer review processes
- Wayne Lutters?
Progress so far
Next (ideas for next steps, open problems)
Surfacing/managing/resolving disagreements in ontologies/terms/federation
- Group page: Forking and Federating
- Discord Channel: #forking-and-federating
What
Who
- Konrad Hinsen and Jonny Saunders: https://discord.com/channels/1029514961782849607/1038988750677606432/1040172075773607956
Progress so far
Next (ideas for next steps, open problems)
Hidden value / mental model mismatches in transitions between workflows / tools
- Group page: Mental Models
- Discord Channel: #mental-models
What
What hidden value / mental (mis)matches might there be between new infrastructures we want to build (e.g., ontology-based organization of knowledge) and existing workflows / tools amongst scientists?
Who
Pooja Upadhyay: https://discord.com/channels/1029514961782849607/1038594946791387276/1039242312615735346
twitter (centralized platform) to mastodon (decentralization, federation)
e.g., ontologies vs. dictionaries